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Crystal structure of GH42 beta-galactosidase BiBga42A from Bifidobacterium longum subspecies infantis E160A/E318A mutant in complex with galactose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293.15 0.1 M MES-NaOH buffer (pH 6.5), 0.1 M (CH3COO)2Mg, 10% PEG 10000, 25% glycerol, 30 mM lacto-N-tetraose (cleaved)
Crystal Properties Matthews coefficient Solvent content 2.64 53.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 234.47 α = 90 b = 182.691 β = 125.73 c = 143.263 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315 2012-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.9 48.57 98.3 0.097 0.058 0.997 9.5 3.7 376638 22.06
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.93 83 0.935 0.672 0.545 1.1 2.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.9 48.61 357918 18712 98.26 0.18935 0.18731 0.1939 0.22841 0.2311 RANDOM 24.001
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -0.54 -0.36 2.4 -0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.393 r_dihedral_angle_2_deg 7.642 r_dihedral_angle_1_deg 6.928 r_long_range_B_refined 4.745 r_long_range_B_other 4.672 r_scangle_other 3.763 r_mcangle_it 2.752 r_mcangle_other 2.752 r_scbond_it 2.453 r_scbond_other 2.453
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.393 r_dihedral_angle_2_deg 7.642 r_dihedral_angle_1_deg 6.928 r_long_range_B_refined 4.745 r_long_range_B_other 4.672 r_scangle_other 3.763 r_mcangle_it 2.752 r_mcangle_other 2.752 r_scbond_it 2.453 r_scbond_other 2.453 r_mcbond_it 1.931 r_mcbond_other 1.931 r_angle_refined_deg 1.405 r_angle_other_deg 0.496 r_chiral_restr 0.069 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 32856 Nucleic Acid Atoms Solvent Atoms 2870 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing